Parasitism in plants is often accompanied by a suite of morphological and physiological changes resulting in a condition known as the ‘parasitic reduction syndrome’. With changes including extreme vegetative reduction, frequently beyond any resemblance to its photosynthetic relatives, accompanied by significant losses of genes linked to photosynthesis, the study of parasitic plants can be challenging. Conopholis (Orobanchaceae) is a small holoparasitic genus distributed across eastern and southwestern North America and Central America. This genus has never been the subject of a molecular phylogenetic or morphometric analyses. In addition, very little is known of the relationships among populations and of their post-glacial history. To investigate the species limits and phylogenetic relationships in Conopholis, we conducted a comprehensive molecular phylogenetic study of the genus as well as a fine-scale morphometric study. Based on plastid and nuclear sequences, Conopholis was found to contain three distinct and well-supported lineages which have varying degrees of overlap with previously proposed taxa. The clustering and ordination analyses of the morphometric study corroborated the molecular data, demonstrating the morphological differentiation between the three lineages detected within Conopholis. A taxonomic re-alignment is proposed for the genus that recognizes three species, C. americana, C. panamensis, and C. alpina. To address genetic diversity and phylogeographic structure of C. americana in eastern North America, microsatellite markers were developed and characterized for the first time in this species. Using these newly generated markers along with sequences from the plastid genome, the persistence of a minimum of two glacial refugia at the last glacial maximum were inferred, one in Florida and southern Alabama and another in the Appalachian Mountains near the southern tip of Blue Ridge Mountains. The diversity seen across the southern Appalachian Mountains supports the hypothesis that populations derived from the southern and northern refugia come together in this area.

Parasitism in plants is often accompanied by a suite of morphological and physiological changes resulting in a condition known as the ‘parasitic reduction syndrome’. With changes including extreme vegetative reduction, frequently beyond any resemblance to its photosynthetic relatives, accompanied by significant losses of genes linked to photosynthesis, the study of parasitic plants can be challenging. Conopholis (Orobanchaceae) is a small holoparasitic genus distributed across eastern and southwestern North America and Central America. This genus has never been the subject of a molecular phylogenetic or morphometric analyses. In addition, very little is known of the relationships among populations and of their post-glacial history. To investigate the species limits and phylogenetic relationships in Conopholis, we conducted a comprehensive molecular phylogenetic study of the genus as well as a fine-scale morphometric study. Based on plastid and nuclear sequences, Conopholis was found to contain three distinct and well-supported lineages which have varying degrees of overlap with previously proposed taxa. The clustering and ordination analyses of the morphometric study corroborated the molecular data, demonstrating the morphological differentiation between the three lineages detected within Conopholis. A taxonomic re-alignment is proposed for the genus that recognizes three species, C. americana, C. panamensis, and C. alpina. To address genetic diversity and phylogeographic structure of C. americana in eastern North America, microsatellite markers were developed and characterized for the first time in this species. Using these newly generated markers along with sequences from the plastid genome, the persistence of a minimum of two glacial refugia at the last glacial maximum were inferred, one in Florida and southern Alabama and another in the Appalachian Mountains near the southern tip of Blue Ridge Mountains. The diversity seen across the southern Appalachian Mountains supports the hypothesis that populations derived from the southern and northern refugia come together in this area.

Made available in DSpace on 2015-04-17T14:55:19Z (GMT). No. of bitstreams: 1 Arquivototal.pdf: 1356123 bytes, checksum: 7115ed47a5956fbd95bdffd700b48424 (MD5) Previous issue date: 2012-11-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Trichogramma species are identified by the morphology of the male genitalia, making the identification difficult due to the small size of the individual (0.25 mm) and/or the presence of cryptic species. Therefore molecular biology constitutes a good alternative for the identification of Trichogramma species and is also used in the identification of Proteobacteria of the genus Wolbachia, known to induce parthenogenesis in Trichogramma species. The purpose of this thesis was to use molecular methods to identify Trichogramma species, verify the diversity of Trichogramma pretiosum populations in 11 cities in Brazil and its association with bacteria of the genus Wolbachia. The samples of Trichogramma pretiosum species and Trichogramma populations were submitted to extraction of genomic DNA for PCR using the forward primer ITS-2- 5 TGTGAACTGCAGGACACATG-3 and the reverse primer IT2-5 GTCTTGCCTGCTCTGCTCTGAG.-3`. The DNA products obtained from Trichogramma species and populations of T. pretiosum were purified and sequenced. To detect the presence of bacteria of the Wolbachia genus in T. pretiosum populations, the amplifications were done using wsp specific primers, with a final reaction volume of 25 μl. The size of PCR products was determined using a molecular weight marker 100 bp using a negative control without DNA, the remaining components and a positive control containing Wolbachia. It can be verified that it was possible to extract DNA from all the Trichogramma species with quantities and qualities sufficient for electrophoretic profiles with genomic DNA concentrations ranging from 15.3 to 50ng/μl. Using PCR, the fragments of the ITS2 region of ribosomal DNA were amplified and one can identify the species of Trichogramma with the sequencing by using the similarity search of the BLAST program in the GenBank database (NCBI - National Center for Biotechnology Information) and dendrogram analysis performed according to the genetic distance matrix, from which three groups were formed, the first by T. exigum, the second by T. pretiosum and the third by T. galloi. With the results of the query by similarity using the BLAST program in the GenBank database a maximum identification average of 92,2% was obtained regarding the species of Trichogramma pretiosum, confirming the correct sequencing. The size of the sequences ranged from 355 to 503 bp. The average G + C content (guanine + cytosine) was 53,2%. After aligning the 11 sequences of T. pretiosum, 391 sites were found conserved, reflecting 73% of the total of 536 sites found, confirming the similarity between samples, as well as confidence in the sequences obtained. The average found for this distance matrix was 0.30. According to the dendrogram obtained from the genetic distance matrix using the neighbor-joining method one can verify the presence of four groups, the first formed by the TPAES, TPPARS, TPRMT TPCVMT populations and the second by the TPSPMT population, the third group by the TPPPE, TPMVCE, TPPPB, TPPPMT, TPJSP populations, and the fourth by the TPPLMT population, being the most genetically distant population. The geographical distance did not affect the genetic similarity or dissimilarity between parasitoids having no significant difference between geographic distance and genetic similarity of the T. pretiosum samples in the locations collected. Of the T. pretiosum populations analyzed, the presence of viii endobacterias occurred in the population from the state of Espírito Santo, the first local record of the presence of this α proteobacteria for the species. / As espécies de Trichogramma são identificadas por meio da morfologia da genitália do macho, sendo dificultada pelo tamanho reduzido do indivíduo (0,25 mm) e/ou a presença de espécies crípticas. Por esta razão, a biologia molecular se constituí em uma boa alternativa para a identificação de espécies de Trichogramma, sendo também utilizada na identificação de proteobactéria do gênero Wolbachia, conhecida por induzir partenogênese em espécies de Trichogramma. O objetivo desta tese foi utilizar métodos moleculares para identificação de espécies de Trichogramma, verificar a diversidade de populações de Trichogramma pretiosum em 11 municípios no Brasil e sua associação com a bactéria do gênero Wolbachia. As amostras de espécies do gênero Trichogramma e de populações de Trichogramma pretiosum foram submetidas à extração de DNA genômico para a realização de PCR utilizando o primer direto ITS-2- 5 TGTGAACTGCAGGACACATG-3 e o reverso IT2-5 GTCTTGCCTGCTCTGCTCTGAG.-3`. Os produtos de DNA obtidos das espécies de Trichogramma e das populações de T. pretiosum foram purificados e submetidos ao seqüenciamento. Para detectar a presença de bactérias do gênero Wolbachia em populações de T. pretiosum, as amplificações foram realizadas com primers específicos wsp, com um volume final da reação de 25 μl. O tamanho dos produtos de PCR foi determinado utilizando um marcador de peso molecular de 100 pb, sendo utilizado um controle negativo sem DNA e o restante dos componentes e um controle positivo com a presença de Wolbachia. Pode-se verificar que foi possível extrair DNA de todas as espécies de Trichogramma estudadas com quantidades e qualidades suficientes para obter perfis eletroforéticos, com concentrações do DNA genômico variando entre 15,3 e 50 ng/μl. Por meio da técnica de PCR, os fragmentos da região ITS2 do DNA ribossomal foram amplificados, sendo possível identificar as espécies de Trichogramma pelo sequenciamento, sendo realizada a busca por similaridade utilizando o programa BLAST, no banco de dados do GenBank (NCBI National Center for Biotechnology Information) e feita a análise de dendrograma de acordo com a matriz de distância genética, onde foi obtido três grupos, o primeiro formado pela espécie T. exigum, o segundo pela espécie T. pretiosum e o terceiro pela espécie T. galloi. Com o resultado da busca por similaridade utilizando o programa BLAST, no banco de dados do GenBank, obteve-se uma média de 92,2% de máxima identificação referente à espécie de Trichogramma pretiosum, confirmando o correto sequenciamento. O tamanho das sequências variaram de 355 a 503 pb. A média do conteúdo G + C (Guanina + Citosina) foi de 53,2%. Após o alinhamento das 11 sequências de T. pretiosum, foram encontrados 391 sítios conservados, que refletem 73 % do total de 536 sítios encontrados, confirmando a semelhança entre as amostras, bem como a confiança nas sequências obtidas. A média encontrada para essa matriz de distância foi de 0,30. De acordo com o dendrograma obtido a partir da matriz de distância genética pelo método do vizinho próximo (Neighbor-Joining), pode-se verificar a presença de quatro grupos: o primeiro, formado pelas populações TPAES, TPPARS, TPRMT e TPCVMT; o segundo, pela população de TPSPMT; o terceiro grupo, pelas populações de TPPPE, TPMVCE, TPPPB, TPPPMT, TPJSP e o quarto pela população de TPPLMT, sendo a população mais distante geneticamente. A distância geográfica não afetou a similaridade ouvi dissimilaridade genética entre os parasitóides, não existindo, diferenças significativas entre distância geográfica e a similaridade genética das amostras de T. pretiosum nas localidades coletadas. Das populações de T.pretiosum analisadas, a presença da endobactérias ocorreu na população proveniente do Estado do Espírito Santo, sendo o primeiro registro local da presença dessa α proteobactéria para a espécie.

A família Accipitridae representa uma das maiores radiações de aves atuais, ocupando habitats diversos em grande parte do planeta. Entre as divisões propostas para a família no passado, o grupo dos gaviões buteoninos figura entre um dos poucos que se aproximam em composição a uma linhagem monofilética, de acordo com análises filogenéticas recentes. Além de ocorrer tanto no Novo Mundo como no Velho Mundo, a maior parte das espécies de gaviões buteoninos está concentrada na América do Sul e na América Central, o que os torna um modelo atrativo para a análise de padrões e processos de diversificação em escalas continental e local. Outro aspecto interessante do grupo é o grande número de espécies migratórias, padrão ainda pouco explorado sob uma perspectiva filogenética. Os principais objetivos deste trabalho foram inferir as relações filogenéticas entre as espécies de gaviões buteoninos, analisar a evolução do comportamento migratório no grupo, e inferir padrões e processos de diversificação, com ênfase na região Neotropical. Foram utilizados mais de 7.000 pares de base de DNA mitocondrial e nuclear de 51 espécies de gaviões buteoninos, compreendendo o maior estudo filogenético do grupo até o momento. Do total de seqüências utilizadas, cerca de um terço foi representado por seqüências de DNA do 12S, tRNAVal e 16S, que contém uma proporção de sítios de evolução dependente resultante da existência de uma estrutura secundária. Como forma de avaliar o impacto destes sítios nas estimativas, foram também realizadas análises alternativas que incorporaram informação de estrutura secundária. Devido à indisponibilidade de um modelo de estrutura secundária de 16S para aves, este foi aqui elaborado com base em uma análise comparativa de representantes de todas as ordens de aves atuais. Os resultados sugerem que os gêneros Buteo, Leucopternis e Buteogallus como atualmente reconhecidos não são monofiléticos, o que ressalta a falta de concordância entre a classificação atual e a histórica evolutiva do grupo. Cinco linhagens principais foram encontradas, sendo a base da árvore composta por espécies predominantemente neotropicais, e a porção mais derivada principalmente por espécies neárticas e do Velho Mundo. Este resultado, associado às estimativas de tempo de divergência, sugere um longo período de diversificação na região Neotropical (com início entre o Oligoceno Superior ou o Mioceno, e se estendendo até o Pleistoceno), com colonização e diversificação recentes na região Neártica e no Velho Mundo (com início no Mioceno Superior ou no Plioceno, se estendendo até o Pleistoceno). O comportamento migratório evoluiu diversas vezes, e pode ter contribuído para a diversificação de algumas espécies, ao possibilitar a colonização de habitats antes não ocupados e promover especiação em ilhas. Na região Neotropical, disjunções de espécies de florestas de terras baixas que ocupam áreas a leste e oeste dos Andes ocorreram quatro vezes, possivelmente em dois eventos vicariantes. As disjunções mais antigas podem ter sido causadas pelo soerguimento da cordilheira, enquanto não foi possível definir claramente os processos envolvidos nas especiações mais recentes. Foram encontradas duas linhagens distribuídas em habitats alagados e ripários. Os resultados sugerem não somente um longo processo de diversificação, de forma independente das espécies de florestas não alagadas, mas também conexões históricas entre florestas de várzea da Amazônia e habitats costeiros. Espécies florestais e de áreas abertas não são reciprocamente monofiléticas. De forma similar, em alguns casos, espécies pertencentes a um mesmo bioma não são proximamente relacionadas, o que sugere uma história complexa de diversificação na região. A utilização de dados de sítios emparelhados de seqüências de RNA não trouxe mudanças significativas nas topologias e inferências de tempo de divergência, possivelmente devido à baixa variação das hastes neste grau de divergência. / The family Accipitridae represents one of the largest radiations of modern birds, with species being found in a plethora of habitats around the world. Among the divisions proposed for the family in the past, the group of the buteonine hawks is one of the few that approximate monophyletic lineages, according to recent phylogenetic analyses. Besides occurring both in the New World and Old World, most buteonine hawk species are mainly found in Central and South America, what provides an opportunity to evaluate patterns and processes of diversification in both continental and local scales. The main goals of this work were to infer phylogenetic relationships among species of buteonine hawks, analyze the evolution of migratory behaviour, and evaluate patterns and processes of diversification, especially in the Neotropical region. We obtained more than 7.000 base pairs of mitochondrial and nuclear DNA sequences from 51 species of buteonine hawks, what comprises the largest phylogenetic analysis of the group so far. Approximately one third of the total dataset was obtained from DNA sequences of 12S, tRNAVal and 16S, which are known to have paired sites that evolve in concert due to the presence of a secondary structure. Alternative analyses incorporating such information have been performed, as a way to evaluate the effects of secondary structure in the phylogenetic analyses. Since a model of secondary structure of 16S of birds was not available so far, we build one based on comparative analysis of representatives of all modern avian orders. The results suggest that the genera Buteo, Leucopternis and Buteogallus as currently accepted are not monophyletic, what stress a lack of concordance between current classification and the evolutionary history of this group. Five main lineages were found, and the most basal part of the topology is composed by mainly neotropical species, while the majority of neartic and Old World species were positioned in the most derived part of the tree. Together with divergence time estimates, those results suggest a long period of diversification in the Neotropics (possibly beginning in the Upper Miocene or Oligocene, and extending to the Pleistocene), with a latter colonization and diversification of the Neartics and Old World (possibly beginning between the Upper Oligocene or Pliocene, and extending to the Pleistocene). Migratory behaviour evolved several times, and may have contributed to diversification by means of exploitation of previously unavailable habitats as well as promotion of speciation in islands. Lowland species disjunctions between each side of the Andes occurred four times, possible due to two vicariant events. The earliest disjunctions may have been caused by Andean orogeny, but no process could be clearly attributed to the two most recent speciations. Two lineages restricted to flooded habitats were found. The results suggest not only a long process of diversification in such habitats, independently of species of non-flooded habitats, but also a historical relationship between várzea forests in Amazonia and costal habitats. Similarly, species that occupy the same biome are not the closest relatives in several cases, what suggests a complex history of diversification in the Neotropical region. Inclusion of secondary structure information did not affect significantly phylogenetic and divergence time estimates, likely due to the low variation in stems in such level of divergence.

O continente sul-americano é a única região biogeográfica onde podemos encontrar um grupo estenohalino de elasmobrânquios: as arraias da família Potamotrygonidae. Entre 19 e 21 espécies de potamotrigonídeos estão taxonomicamente organizadas em três gêneros, distribuídas pelas bacias dos rios Atrato, Magdalena, Maracaibo, Orinoco, Essequibo, Amazonas e do Prata, os quais desembocam no Oceano Atlântico e no Mar do Caribe. Diversos cenários biogeográficos postulados para explicar a presença de linhagens predominantemente marinhas nos sistemas fluviais da América do sul foram propostos. O mais aceito para a origem e diversificação de Potamotrygonidae é a de invasão de um ancestral caribenho no sistema fluvial sul-americano durante as ingressões marinhas do Mioceno inferior no noroeste do continente, seguido de isolamento por alteração dos padrões de drenagens do Orinoco e formação dos Andes. A fauna parasitária de Potamotrygonidae está representada predominantemente por membros de Cercomeromorpha, um clado composto por linhagens de platelmintos membros de Cestoda e Monogenoidea. Dois gêneros de monogenóideos parasitas branquiais podem ser encontrados em potamotrigonídeos: Potamotrygonocotyle (Monocotylidae), para o qual 12 espécies são conhecidas, e a monotípica Paraheteronchocotyle amazonense (Hexabothriidae). O objetivo desta tese é propor uma hipótese de relacionamento filogenético baseada em dados moleculares para as espécies de Potamotrygonocotyle, e discutir padrões de evolução da espécie P. aramasae e seu hospedeiro Paratrygon aiereba, distribuídos em diferentes rios amazônicos. Sequências nucleotídicas do gene mitocondrial cox1 e nuclear ITS1 foram utilizadas simultaneamente em uma busca de uma hipótese filogenética para todas as espécies conhecidas de Potamotrygonocotyle. Os resultados recuperaram o status monofilético de cinco espécies, sugeriram complexos de linhagens crípticas para três espécies nominais e revelaram relacionamentos de grupo-irmão não detectados na hipótese filogenética mais recente para o gênero, baseada em dados morfológicos. Adicionalmente, os resultados apresentados suportam decisões taxonômicas recentes envolvendo sinonímias entre espécie nominais de Potamotrygonocotyle. Finalmente, os relacionamentos filogenéticos de haplótipos de diferentes populações de P. aramasae e seu hospedeiro P. aiereba foram acessados pela análise cladística de múltiplos marcadores mitocondriais, com o objetivo de se detectar possíveis padrões filogeográficos e testá-los sob predições filogenéticas de três hipóteses de diversificação amazônica (Hidrogeológica, de Museu e Paleogeográfica). Sequências dos genes ribossomal 16S e citocromo oxidase 1 foram obtidas para espécimes de parasitas de seis sub-bacias amazônicas. Os hospedeiros foram amostrados em 10 sub-bacias amazônicas e na sub-bacia do rio Essequibo, para os quais foram obtidas sequências nucleotídicas dos genes mitocondriais citocromo oxidase 1, citocromo b e ATPase. Os resultados sugerem a ausência de padrões filogeográficos para o parasita, cujos resultados indicam um modelo de alta dispersão. Em contraste, P. aireba é caracterizada por populações bem estruturadas, de acordo com as sub-bacias amostradas. O padrão filogeográfico geral desta espécie é concordante com as predições da Hipótese de Museu (linhagens mais antigas em rios dos escudos pré-cambrianos; linhagens apicais na bacia sedimentar amazônica). / South America is the only biogeographical region in the world where is possible to find an exclusive stenohalin group of elasmobranchs: the Potamotrygonidae stingrays. Between 19 and 21 species of potamotrygonid stingrays are taxonomically organized in three genera, distributed in the Atrato, Magdalena, Maracaibo, Orinoco, Essequibo, Amazonas e la Plata river Basins, discharging in both Atlantic and Caribbean waters. Distinct biogeographical scenarios have been proposed to explain the presence of predominantly marine lineages in the south American fluvial systems. The most accepted theory for Potamotrygonidae is the invasion of a Caribbean ancestor in the south-American freshwater system during the marine ingression of the early Miocene in the northwest of the continent, followed by its isolation due alterations of Orinoco rivers drainage patterns, as well as formation of Andes. The parasitic fauna of potamotrygonids is predominantly represented by members of Cercomeromorpha, a clade composed by members of Cestoda and Monogenoidea. Two genera of gill parasites monogenoidean might be found in potamotrygonids: Potamotrygonocotyle (Monocotylidae), for which 12 species are currently recognized, and the monotypic Paraheteronchocotyle amazonense (Hexabothriidae). The goal of this study is to propose a phylogenetic hypothesis based in molecular data for members of Potamotrygonocotyle, as well as to discuss evolutionary patterns of the species P. aramasae and its host Paratrygon aiereba, distributed through different amazon rivers. Nucleotide sequences of the mitochondrial gene cox1, and the nuclear gene ITS1 were simultaneously used to infer phylogenetic sister-group relationships among allrecognized species of Potamotrygonocotyle. The results recovered the monophyletic status of five species, suggested cryptic lineages for three species complexes, and revealed sister-groups relationships not detected previously by the phylogenetic analysis of morphological data. Additionally, the results supports recent taxonomic decisions involving synonyms among nominal species within the genus. The phylogenetic relationships of haplotypes from distinct populations of the parasite P. aramasae, as well as from its host Paratrygon aiereba, were accessed by the cladistic analysis of mitochondrial markers, in an attempt of detecting possible phylogeographic patterns, and to test them against phylogenetic predictions of three amazonian bio-diversification hypotheses (Hydrogeology, Museum, Paleogeography). Sequences of the ribosomal 16S gene and cytochrome oxidase 1 were obtained from parasite specimens collected in six amazon sub-basins. The hosts were sampled in 10 amazon sub-basins, as well as in the Essequibo sub-basin, for which cythocrome oxidase 1, cythocrome b, and ATPase sequences were obtained. No clear phylogeographic patterns were revealed for theparasite haplotypes, and the results suggest a high dispersion model. In contrast, P. aiereb is characterized by strongly structured populations, according to the sub-basin sampled. The general phylogeographic pattern recovered for this species is in agreement with the Museum Hypothesis predictions (older lineages in rivers of the pre-cambrian shields; apical lineages inhabiting the sedimentary amazon basin).

Orientador: Valéria Maia Merzel / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T08:23:29Z (GMT). No. of bitstreams: 1 GonzalesLimache_ElmerErasmo_M.pdf: 2196065 bytes, checksum: 46f92b130d253afebe31e1385f5a430b (MD5) Previous issue date: 2015 / Resumo: A água residuária da extração de petróleo é altamente salina e contém uma mistura complexa de hidrocarbonetos, muitos dos quais são altamente tóxicos. Com o aumento da preocupação em preservar o meio ambiente, as tecnologias baseadas em processos biológicos para o tratamento das águas de efluentes estão recebendo atenção especial por serem mais econômicas e versáteis. No entanto, tais processos são influenciados por fatores, tais como: pH, temperatura, salinidade e pressão. Condições extremas destes fatores podem matar ou inibir espécies que não estejam adaptadas. O presente trabalho teve como objetivos identificar e caracterizar 141 bactérias isoladas de águas de produção e lodos ativados do Terminal Marítimo Almirante Barroso (TEBAR-SP) utilizando técnicas de taxonomia molecular, e avaliar o potencial de biodegradação frente a distintos hidrocarbonetos do petróleo, sob condições de hipersalinidade. O DNA genômico extraído de todos os isolados foi utilizado em reação de PCR para amplificação do gene que codifica para o RNAr 16S. O sequenciamento e a análise filogenética do gene RNAr 16S revelaram que estes isolados pertenciam a 20 gêneros distintos, Idiomarina (48), Halomonas (32), Marinobacter (20), Modicisalibacter (3), Arhodomonas (2), Vibrio (1), Pseudoalteromonas (1), Shewanella (1), Alcanivorax (3), Nitratireductor (2), Marispirillum (2), Thioclava (1), Martelella (2), Pusillimonas (2), Brevibacterium (6), Dietzia (3), Rhodococcus (2), Bacillus (2), Staphylococcus (2) e Salegentibacter (4). O método de tipagem molecular RAPD (Random Amplified Polymorphic DNA) foi utilizado para diferenciar os isolados em nível infra-específico, permitindo identificar 49 perfis genéticos diferentes entre os 141 isolados. Os resultados obtidos no presente estudo demonstraram uma alta diversidade taxonômica da fração cultivada da comunidade de bactérias aeróbias presente em águas de produção e lodos ativados, assim como uma alta capacidade dos isolados para suportar concentrações elevadas de salinidade. A habilidade dos isolados para degradar hidrocarbonetos sob condições de hipersalinidade foi avaliada por cromatografia gasosa. Os resultados evidenciaram a preferência das bactérias pela biodegradação de hidrocarbonetos aromáticos / Abstract: The wastewater from oil extraction is highly saline and contains a complex mixture of hydrocarbons, many of which are highly toxic. With the increasing concern to preserve the environment, technologies based on biological processes for the treatment of wastewater are receiving special attention, since they are more economical and versatile, however, such processes are influenced by factors such as pH, temperature, salinity and pressure. Extreme conditions of these factors can kill or inhibit species not adapted to such environments. This study aimed to identify and characterize 141 bacteria isolated from production water and activated sludge derived from Ferry Terminal Almirante Barroso (TEBAR-SP) using molecular taxonomy techniques, and to evaluate the potential for biodegradation of distinct oil hydrocarbons under hypersaline conditions. Genomic DNA extracted from all isolates were used in PCR reactions for amplification of the gene coding for 16S rRNA. The sequencing and phylogenetic analysis of the 16S rRNA gene revealed that these isolates belonged to the following 20 different genera: Idiomarina (48), Halomonas (32), Marinobacter (20), Modicisalibacter (3), Arhodomonas (2), Vibrio (1), Pseudoalteromonas (1), Shewanella (1), Alcanivorax (3), Nitratireductor (2), Marispirillum (2), Thioclava (1), Martelella (2), Pusillimonas (2), Brevibacterium (6), Dietzia (3), Rhodococcus (2), Bacillus (2), Staphylococcus (2) and Salegentibacter (4). The molecular typing method RAPD (Random Amplified Polymorphic DNA) was used to differentiate isolates at the infra-specific level, allowing the identification of 49 different genetic profiles out of 141 isolates. The results obtained in this study demonstrated a high taxonomic diversity of the cultivated fraction of the aerobic bacterial community present in production waters and activated sludge, as well as a high capacity of the individual members to support high levels of salinity. The ability of the isolates to degrade hydrocarbons under hypersaline conditions was evaluated by gas chromatography. The results showed the preference of bacteria by biodegradation aromatic hydrocarbon compounds / Mestrado / Genetica de Microorganismos / Mestre em Genética e Biologia Molecular

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Made available in DSpace on 2016-06-02T19:29:23Z (GMT). No. of bitstreams: 1 3030.pdf: 2014938 bytes, checksum: b6d8f7597811d1909e335b6facc588b7 (MD5) Previous issue date: 2010-03-26 / Universidade Federal de Minas Gerais / The catfishes of the Pseudoplatystoma genus are carnivore pimelodids, migratory and important for fisheries in all major river basins from South America. Only three species were recognized for the genus (P. corruscans, P. fasciatum and P. tigrinum), but a new revision raised to eight the number of species (P. fasciatum, P. punctifer, P. orinocoense, P. magdaleniatum, P. reticulatum, P. tigrinum, P. metaense and P. corruscans). Recently, Pseudoplatystoma was the subject of a molecular phylogeny study based on mitochondrial markers, where monophyletic clades where found for P. tigrinum, P. corruscans, P. reticulatum+P. punctifer+P. fasciatum and P. magdaleniatum. Despite these advances on the knowledge of the evolutionary history and systematics of the group, there are still questions to be answered. Thus, this study aimed a molecular phylogenetic analysis on Pseudoplatystoma to try to answer pendant questions about the systematics and taxonomy of the group, and propose a scenario for its diversification history in the geographic area of South America. In order to do this, we employed the mitochondrial Cytochrome b gene and introns from Rag1 and S7 genes, whose phylogenies were estimated by Maximum Likelihood using TREEFINDER software. Nodes were dated on BEAST software. It was shown that some Pseudoplatystoma species, resulting from the last revision of the genus, do not correspond to monophyletic groups or they were not significantly supported clades in all trees. The only monophyletic species in all markers were P. magdaleniatum and P. corruscans. Pseudoplatystoma orinocoense was a monophyletic lineage only on Cytochrome b. In light of these results, it is suggested that the old terminology P. fasciatum to be revalidated for the taxa here defined as P. fasciatum clade: P. punctifer (Amazon, Maranhão, Tocantins-Araguaia), P. reticulatum (Paraná-Paraguay) and P. fasciatum (Guyanas). Under the same rationale, P. tigrinum should be revalidated for Orinoco, given the paraphyletism of P. metaense. However, some cases of nonmonophyletic species in one or more markers may be due to incomplete lineage sorting, although this possibility needs to be investigated using other markers. The history of diversification of Pseudoplatystoma was the result of millions of years of evolution and and it was strongly influenced by the evolution of the South America geographical matrix. The biogeographic study allowed us to identify and date the important diversification events for the genus and relate them to the historical geomorphological and/or climate changes reported for South America, which would be the primary diversification causes for other freshwater fishes from the continent. / Os bagres do gênero Pseudoplatystoma são pimelodídeos carnívoros, migradores e de importância pesqueira em todas as grandes bacias hidrográficas da América do Sul. Apenas três espécies eram reconhecidas para o gênero (P. corruscans, P. fasciatum e P. tigrinum), mas uma nova revisão elevou para oito o número de espécies (P. fasciatum, P. punctifer, P. orinocoense, P. magdaleniatum, P. reticulatum, P. tigrinum, P. metaense e P. corruscans). Recentemente, Pseudoplatystoma foi alvo de um de estudo de filogenia molecular com marcadores mitocondriais, onde foram encontrados clados monofiléticos para P. tigrinum, P. corruscans, P. reticulatum+P. punctifer+P. fasciatum e P. magdaleniatum. Apesar desses avanços no conhecimento da história evolutiva e da sistemática do grupo, ainda restam questões a serem respondidas. Dessa forma, o presente estudo objetivou uma análise filogenética molecular em Pseudoplatystoma para tentar responder questões pendentes sobre a sistemática e taxonomia do grupo, bem como propor um cenário para sua história de diversificação no espaço geográfico da América do Sul. Para isso, foram empregados o gene mitocondrial do Citocromo b e íntrons dos genes Rag1 e S7, cujas filogenias foram estimadas por Máxima Verossimilhança no programa TREEFINDER. Os nós das filogenias foram datados no programa BEAST. Foi demonstrado que algumas espécies de Pseudoplatystoma, resultantes da última revisão do gênero, não correspondem a grupos monofiléticos ou não tiveram clados significativamente sustentados em todas as árvores. As únicas espécies monofiléticas em todos os marcadores foram P. magdaleniatum e P. corruscans. Pseudoplatystoma orinocoense só foi uma linhagem monofilética no Citocromo b. À luz desses resultados, sugere-se que a antiga terminologia P. fasciatum seja revalidada para os táxons do clado aqui definido como clado P. fasciatum: P. punctifer (Amazonas, Maranhão, Tocantins-Araguaia), P. reticulatum (Paraná-Paraguai) e P. fasciatum (Guianas). Sob a mesma racionalidade, P. tigrinum deveria ser revalidado para o Orinoco, dado o parafiletismo de P. metaense. Entretanto, alguns dos casos de espécies não-monofiléticas em um ou mais marcadores podem ser devidos à separação incompleta de linhagens, embora essa possibilidade necessite ser investigada com o uso de outros marcadores. A história da diversificação de Pseudoplatystoma foi resultado de milhões de anos de evolução e fortemente influenciada pela evolução da matriz geográfica Sul-Americana. O estudo biogeográfico nos permitiu identificar e datar os eventos de diversificação importantes para o gênero e relacioná-los às mudanças geomorfológicas e/ou climáticas históricas conhecidas para a América dos Sul, que seriam as causas primárias de diversificação de outros peixes de água doce do continente.

Des prospections réalisées en Equateur (Amazonie et côte pacifique) ont permis la collecte d'un matériel entomologique abondant et diversifié, notamment chez les Psychodopygina. Nos travaux ont permis de réaliser plusieurs travaux de systématique, essentiellement moléculaire. Afin de tester les hypothèses phylogénétiques développées par Galati (2010), nous avons conduit une étude de phylogénie moléculaire chez les Psychodopygina. Basée sur les séquences des domaines D1, C2 et D2 de l'ADNr 28S et sur celles d'une partie du cytochrome b de l'ADNmt, elle inclut 49 espèces représentant les sept genres de la sous tribu et la majorité des sous-genres et séries. Les marqueurs ribosomiques sont mieux adaptés à la problématique que le marqueur mitochondrial. Le genre Psychodopygus est monophylétique. En raison du positionnement de Ny. richardwardi parmi les Trichophoromyia, nous concluons à la paraphylie des genres Nyssomyia et Trichophoromyia. Le genre Psathyromyia est également paraphylétique, tout comme le genre Martinsmyia. Le genre Bichromomyia serait le groupe frère du genre Psychodopygus et la validité du genre Vianniamyia, inclus dans le genre Psathyromyia doit être discutée. Des phylogénies moléculaires plus terminales ont été réalisées par comparaison de séquences de l'ITS2, de l'EF-1α et du cytochrome b.Chez les Psychodopygus de la série Guyanensis, une étude moléculaire couplée à une étude morphologique et morphométrique de morphotypes différents chez Ps. geniculatus, en sympatrie avec Ps. corossoniensis et Ps. luisleoni nous a conduit à décrire une espèce nouvelle pour la science : Ps. francoisleponti.Chez Pa. aragaoi, notre étude pilote basée sur l'analyse de morphotypes différents allopatriques et sympatriques renforce l'hypothèse de l'existence probable d'un complexe d'espèces chez ce taxon. Chez Ny. trapidoi, les analyses moléculaires et enzymatiques conduites sur des exemplaires clairs et foncés ne supportent pas la mise en évidence de deux populations comme cela avait été auparavant démontré. Nos approches épidémiologiques ont permis de mettre en évidence l'ADN d'Endotrypanum monterogeii chez plusieurs exemplaires de Ny. trapidoi. Si aucun phlebovirus n'a été détecté dans les échantillons étudiés, nous rapportons la présence d'un flavivirus chez Pa. abonnenci. Mots-clés: Psychodopygina, Equateur, ADN ribosomique, ADN mitochondrial, phylogénie, Endotrypanum. / Most Ecuadorian sand flies studied so far belong to Psychodopygina sub tribe and the present research uses morphometric and modern molecular techniques to answer many some questions regarding this taxon in Ecuador. We present phenetic and phylogenetic analyses based on the sequences of the domains D1, C2 and D2 of the 28S rDNA and cytochrome b mtDNA were used to test the classification of Psychodopygina sub tribe proposed by Galati (2010). Our study includes 49 species representing the seven genera included in the sub tribe and its main subgenera and series. The results support the monophyly of the genus Psychodopygus. The genera Psathyromyia, Nyssomyia and Trichophoromyia are paraphyletic. Bichromomyia is the sister group of Psychodopygus and the validity of the genus Viannamyia is doubtful because it is included inside the Psathyromyia genus. Our data strongly suggest the presence of two populations within Ps. geniculatus and the lack of intermediate forms between these two morphotypes incited us to describe a new sympatric species, Psychodopygus francoisleponti.We also carried out a pilot study based on the analysis of different allopatric and sympatric morphotypes of Pa. aragaoi which suggested the existence of a possible complex of species in this taxa.Finally, we analyzed of mitochondrial gene sequences and isoenzymes from Ny. trapidoi collecte from Ecuador and our result did not support the existence of two sibling species within as previously reported in the literature. From an epidemiological point of view, we emphasize the probable vectorial role of Nyssomyia trapidoi for Endotrypanum monterogeii. Moreover, no phlebovirus was detected in the processed sand flies whereas a flavivirus has been found in a pool of Psathyromyia. abonnenci females.Key words: Psychodopygina, Ecuador, ribosomal DNA, mitochondrial DNA, phylogeny, Endotrypanum.

The group of pleurocarpous mosses comprises approximately 5000 species, which corresponds to about half of all mosses. The pleurocarpous mosses (i.e. “the Core Pleurocarps”) form a monophylum, which consists typically of perennial mosses with creeping stems and abundant lateral branches. In pleurocarpous mosses the archegonium and thus also sporophyte development is restricted to the apices of short, specialized lateral branches, in contrast to most other mosses, where archegonia and sporophytes develop terminally on the main axis (acrocarpous) or on major branches (cladocarpous). Traditionally, pleurocarpous mosses have been divided into three orders based mainly on their sporophytic characters. Brotherus described the Neckeraceae in 1925 and placed it into the Leucodontales, later the family has alternatively been divided into two or three separate families: the Thamnobryaceae, the Neckeraceae and the Leptodontaceae. These families have been placed even in different orders (Neckeraceae and Leptodontaceae among the leucodontalean mosses and Thamnobryaceae among hypnalean mosses) according to their peristome structure and the grade of peristome reduction. A growing amount of evidence indicates that a grouping based on sporophytic characters is artificial and based on convergent evolution. According to the latest phylogenetic studies of pleurocarpous mosses, based on molecular data, the Neckeraceae belong to the order Hypnales and share a sister group relationship with the Lembophyllaceae. In the most recent comprehensive classification 28 genera were included in the Neckeraceae family. This classification was based on both morphological and molecular data, but done with limited taxon sampling that did not cover all species of the family. Some previous studies based on molecular data have challenged the family concept of the Neckeraceae, indicating the need for a revision of the family. Here the family concept of the Neckeraceae is revisited, the closest relatives of the family are resolved and its position within pleurocarpous mosses is shown. In addition, new insights into the morphological evolution of the family are provided. Previous phylogenetic studies indicated that branch lengths among pleurocarpous mosses are usually extremely short. Therefore we chose to use mainly non-coding DNA sequences from rapidly evolving DNA regions. The phylogenetic reconstructions are based on extensive sequence data from all genomes: plastid trnS-trnF and rpl16, nuclear ITS1 & 2 and mitochondrial nad5. Both parsimony (PAUP and PRAP2) and Bayesian statistics (MrBayes) were employed for phylogenetic reconstructions. In order to use the information provided by length mutations indels were included in the analyses as binary data using a simple indel coding approach. No severe conflicts appeared between the different methods used, but the indel coding affected the support values of the inferred topologies. Therefore, all support values resulting from different methods are shown along the phylogenetic trees. The morphological features are studied and synapomorphies for each clade formed in the phylogenetic analyses are interpreted. A new delimitation of the family makes it necessary to reconsider the relevance of the morphological description and the morphological features characteristic of the family need to be reconsidered. Due to new groupings, some changes in the morphological circumscriptions of the genera are necessary, resulting in two new genera and several new combinations. Chapter 1 gives a broad overview of the relationships of the pleurocarpous mosses and shows the need for changes in the definition of genera, families and the corresponding nomenclature in this group. Chapter 2 is a population genetic study on the genus Thamnobryum. The main aim of this chapter is to test the species concept in Thamnobryum that are endemic to strictly restricted regions showing only minor differences in the morphological features in comparison to some more common species. In Chapter 3 the monophyly of the Neckeraceae is tested. In addition, in this chapter the ancestral character states of some morphological characters within the Neckeraceae are reconstructed. Chapters 4 and 5 resolve the genus composition and the relationships within the family in more detail. The results of this thesis show that the Neckeraceae need re-circumscription; this includes changes in the genus composition. The Lembophyllaceae is confirmed to be the sister group of the Neckeraceae. In addition to the new phylogeny, the potential evolution of several characters as a result of environmental selection pressures is analyzed. From the ancestral state reconstructions made (using BayesTraits) for both the habitat and a selection of morphological characters, character state distributions and habitat shift appear congruent, peristome reduction being a good example. However, some character states do not correlate with the habitat, suggesting very complex evolutionary patterns underlying these morphological characters. Many widely distributed genera that are composed of several species and seem to be morphologically coherent (Echinodium, Homalia, Thamnobryum, partly Neckera), are shown in this thesis to be polyphyletic. They are replaced by smaller, geographically more restricted genera that at least in some cases (e.g. Thamnomalia, Homalia s.str., Neckera s.str.) seem to form morphologically heterogeneous genera. In other words, morphology can be misleading in the family Neckeraceae even at the genus level and convergent evolution in both morphological and sequence level characters are common within the family. Special habitat conditions have been shown to result in similar morphological structures also in several other moss groups. This kind of convergent evolution occurs in aquatic mosses, and seems to have occurred among the neckeraceous species Thamnobryum alopecurum and its allies. However, similar morphological structure in similar aquatic habitats can also be due to true phylogenetic relationships as is the case within the Neckeraceae for Handeliobryum sikkimense and Hydrocryphae wardii, or the members of Touwia. The geographical grouping seems to be more strongly correlated with the phylogenetic grouping than thought before.